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Zinc in PDB 8jh4: Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome

Enzymatic activity of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome

All present enzymatic activity of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome:
2.7.7.6;

Other elements in 8jh4:

The structure of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome (pdb code 8jh4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome, PDB code: 8jh4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8jh4

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:61.2
occ:1.00
 SG A:CYS67 1.8 48.6 1.0
NE2 A:HIS80 2.1 22.6 1.0
CB A:CYS67 2.3 48.6 1.0
SG A:CYS77 2.3 28.7 1.0
SG A:CYS70 2.4 37.5 1.0
CD2 A:HIS80 2.7 22.6 1.0
CE1 A:HIS80 3.3 22.6 1.0
CB A:CYS70 3.5 37.5 1.0
CB A:CYS77 3.8 28.7 1.0
CA A:CYS67 3.8 48.6 1.0
CA A:GLY59 3.9 33.0 1.0
N A:CYS70 4.0 37.5 1.0
CG A:HIS80 4.0 22.6 1.0
ND1 A:HIS80 4.3 22.6 1.0
CA A:CYS70 4.3 37.5 1.0
C A:CYS67 4.5 48.6 1.0
CA A:CYS77 4.6 28.7 1.0
N A:SER60 4.6 52.0 1.0
CB A:THR69 4.7 37.0 1.0
N A:GLY79 4.7 22.7 1.0
N A:CYS67 4.7 48.6 1.0
O A:CYS67 4.8 48.6 1.0
N A:THR69 4.8 37.0 1.0
N A:GLY59 4.8 33.0 1.0
C A:GLY59 4.8 33.0 1.0
C A:THR69 4.8 37.0 1.0
CD A:PRO78 4.9 23.2 1.0
CA A:GLY79 4.9 22.7 1.0

Zinc binding site 2 out of 8 in 8jh4

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:210.9
occ:1.00
 SG A:CYS148 2.1 107.0 1.0
SG A:CYS107 2.3 81.5 1.0
CB A:CYS148 2.4 107.0 1.0
SG A:CYS168 2.4 97.6 1.0
SG A:CYS110 2.5 88.0 1.0
CB A:CYS107 3.3 81.5 1.0
CB A:CYS168 3.6 97.6 1.0
N A:CYS168 3.8 97.6 1.0
CA A:CYS148 3.9 107.0 1.0
CB A:CYS110 3.9 88.0 1.0
O A:CYS148 4.2 107.0 1.0
CA A:CYS168 4.3 97.6 1.0
C A:CYS148 4.5 107.0 1.0
N A:GLY169 4.5 98.8 1.0
N A:CYS110 4.6 88.0 1.0
N A:CYS148 4.7 107.0 1.0
CA A:CYS107 4.7 81.5 1.0
CA A:CYS110 4.8 88.0 1.0
C A:CYS168 4.9 97.6 1.0

Zinc binding site 3 out of 8 in 8jh4

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:74.7
occ:1.00
 SG B:CYS1163 1.9 26.1 1.0
SG B:CYS1185 2.3 48.1 1.0
SG B:CYS1182 2.6 42.4 1.0
SG B:CYS1166 2.6 30.1 1.0
CB B:CYS1163 2.8 26.1 1.0
CB B:CYS1166 3.0 30.1 1.0
CB B:CYS1185 3.2 48.1 1.0
N B:CYS1166 3.4 30.1 1.0
CB B:CYS1182 3.4 42.4 1.0
CA B:CYS1166 3.8 30.1 1.0
CA B:CYS1163 4.2 26.1 1.0
N B:CYS1185 4.3 48.1 1.0
CA B:CYS1185 4.4 48.1 1.0
CB B:ILE1165 4.4 32.7 1.0
C B:ILE1165 4.5 32.7 1.0
C B:CYS1166 4.6 30.1 1.0
N B:ILE1165 4.7 32.7 1.0
C B:CYS1163 4.7 26.1 1.0
N B:GLY1167 4.7 23.0 1.0
CA B:ILE1165 4.8 32.7 1.0
CG2 B:ILE1165 4.8 32.7 1.0
CA B:CYS1182 4.9 42.4 1.0
O B:CYS1163 4.9 26.1 1.0
ND2 B:ASN1187 4.9 46.0 1.0

Zinc binding site 4 out of 8 in 8jh4

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:176.9
occ:1.00
 SG C:CYS91 2.2 89.3 1.0
SG C:CYS94 2.2 66.7 1.0
SG C:CYS85 2.3 95.5 1.0
SG C:CYS87 2.4 96.3 1.0
CB C:CYS85 3.2 95.5 1.0
CB C:CYS91 3.5 89.3 1.0
N C:CYS91 3.6 89.3 1.0
CB C:CYS87 3.7 96.3 1.0
CB C:CYS94 3.7 66.7 1.0
O C:CYS91 3.8 89.3 1.0
CA C:CYS91 3.9 89.3 1.0
C C:CYS91 4.0 89.3 1.0
N C:CYS94 4.2 66.7 1.0
CB C:GLU93 4.4 86.3 1.0
C C:TYR90 4.5 87.5 1.0
CA C:CYS85 4.5 95.5 1.0
CA C:CYS94 4.5 66.7 1.0
N C:GLU93 4.7 86.3 1.0
N C:CYS87 4.8 96.3 1.0
C C:CYS85 4.8 95.5 1.0
CA C:CYS87 4.9 96.3 1.0
C C:GLU93 4.9 86.3 1.0
CA C:TYR90 4.9 87.5 1.0
CA C:GLU93 4.9 86.3 1.0
OE1 C:GLU93 5.0 86.3 1.0
O C:CYS85 5.0 95.5 1.0
N C:ASP92 5.0 82.3 1.0

Zinc binding site 5 out of 8 in 8jh4

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:169.8
occ:1.00
 SG I:CYS103 2.1 100.2 1.0
SG I:CYS75 2.3 110.7 1.0
CB I:CYS103 2.4 100.2 1.0
CB I:CYS75 2.8 110.7 1.0
SG I:CYS106 3.0 107.7 1.0
SG I:CYS78 3.2 113.9 1.0
CA I:CYS103 3.9 100.2 1.0
CA I:CYS75 3.9 110.7 1.0
CB I:SER80 4.3 110.8 1.0
OG I:SER80 4.3 110.8 1.0
CE1 I:PHE110 4.3 101.4 1.0
N I:CYS78 4.4 113.9 1.0
CB I:GLU77 4.5 112.1 1.0
N I:CYS106 4.6 107.7 1.0
C I:CYS75 4.6 110.7 1.0
CB I:CYS106 4.7 107.7 1.0
N I:CYS103 4.7 100.2 1.0
CD1 I:PHE110 4.7 101.4 1.0
C I:CYS103 4.7 100.2 1.0
CB I:CYS78 4.7 113.9 1.0
O I:LYS108 4.8 99.8 1.0
CB I:ASN105 4.8 109.6 1.0
N I:GLU77 4.9 112.1 1.0
N I:SER80 4.9 110.8 1.0
N I:CYS75 5.0 110.7 1.0

Zinc binding site 6 out of 8 in 8jh4

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:217.7
occ:1.00
 CB I:CYS29 1.7 120.1 1.0
SG I:CYS29 2.1 120.1 1.0
SG I:CYS32 2.8 119.3 1.0
CA I:CYS29 2.9 120.1 1.0
CD2 I:LEU14 3.3 123.4 1.0
SG I:CYS7 3.4 120.4 1.0
N I:CYS29 3.7 120.1 1.0
CB I:CYS7 3.8 120.4 1.0
C I:CYS29 4.1 120.1 1.0
O I:TYR34 4.2 111.9 1.0
CB I:CYS32 4.5 119.3 1.0
CB I:TYR34 4.6 111.9 1.0
N I:CYS32 4.6 119.3 1.0
CD2 I:TYR34 4.7 111.9 1.0
N I:ARG30 4.7 116.2 1.0
O I:CYS29 4.8 120.1 1.0
C I:SER28 4.8 111.9 1.0
CG I:LEU14 4.8 123.4 1.0
CA I:CYS7 4.8 120.4 1.0
C I:TYR34 5.0 111.9 1.0
N I:TYR34 5.0 111.9 1.0
CA I:CYS32 5.0 119.3 1.0
CB I:CYS10 5.0 120.4 1.0

Zinc binding site 7 out of 8 in 8jh4

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:73.0
occ:1.00
 SG J:CYS44 2.0 20.2 1.0
SG J:CYS7 2.2 20.2 1.0
SG J:CYS10 2.6 20.2 1.0
SG J:CYS45 2.7 20.2 1.0
N J:CYS45 3.1 20.2 1.0
CB J:CYS44 3.1 20.2 1.0
CB J:CYS7 3.4 20.2 1.0
C J:CYS44 3.6 20.2 1.0
CA J:CYS45 3.6 20.2 1.0
CB J:CYS10 3.6 20.2 1.0
CB J:CYS45 3.7 20.2 1.0
N J:CYS10 3.8 20.2 1.0
CA J:CYS44 3.9 20.2 1.0
CA J:CYS10 4.3 20.2 1.0
CB J:SER9 4.3 19.9 1.0
O J:CYS44 4.3 20.2 1.0
NE J:ARG42 4.5 25.7 1.0
N J:CYS44 4.7 20.2 1.0
C J:SER9 4.7 19.9 1.0
CA J:CYS7 4.7 20.2 1.0
N J:SER9 4.8 19.9 1.0
N J:GLY11 4.8 14.4 1.0
CA J:SER9 4.8 19.9 1.0
CB J:ARG42 4.8 25.7 1.0
OG J:SER9 4.9 19.9 1.0
NH1 J:ARG42 5.0 25.7 1.0
C J:CYS10 5.0 20.2 1.0

Zinc binding site 8 out of 8 in 8jh4

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Elongation Complex Containing 60 Bp Upstream Dna Loop, Stalled at Shl(-1) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:218.2
occ:1.00
 SG L:CYS50 2.2 93.3 1.0
SG L:CYS33 2.2 71.3 1.0
CB L:CYS50 2.3 93.3 1.0
SG L:CYS53 2.4 110.4 1.0
CB L:CYS33 2.9 71.3 1.0
CB L:HIS55 3.4 62.1 1.0
N L:HIS55 3.5 62.1 1.0
CA L:CYS50 3.8 93.3 1.0
SG L:CYS36 3.8 86.3 1.0
CA L:HIS55 4.0 62.1 1.0
CA L:CYS33 4.1 71.3 1.0
CB L:CYS53 4.1 110.4 1.0
N L:GLY54 4.2 85.1 1.0
N L:CYS53 4.3 110.4 1.0
N L:CYS36 4.4 86.3 1.0
C L:CYS50 4.4 93.3 1.0
CG L:HIS55 4.5 62.1 1.0
N L:CYS50 4.6 93.3 1.0
N L:GLY34 4.6 55.2 1.0
O L:HIS55 4.6 62.1 1.0
CA L:CYS53 4.6 110.4 1.0
N L:ALA35 4.6 64.6 1.0
C L:GLY54 4.7 85.1 1.0
C L:HIS55 4.7 62.1 1.0
CB L:CYS36 4.7 86.3 1.0
CB L:ALA35 4.7 64.6 1.0
C L:CYS33 4.8 71.3 1.0
C L:CYS53 4.8 110.4 1.0
CA L:GLY54 4.9 85.1 1.0
N L:LYS51 4.9 104.2 1.0
O L:CYS50 5.0 93.3 1.0

Reference:

M.Akatsu, H.Ehara, T.Kujirai, R.Fujita, T.Ito, K.Osumi, M.Ogasawara, Y.Takizawa, S.I.Sekine, H.Kurumizaka. Cryo-Em Structures of Rna Polymerase II-Nucleosome Complexes Rewrapping Transcribed Dna J.Biol.Chem. 05477 2023.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2023.105477
Page generated: Thu Dec 28 13:21:32 2023

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